You have full control over all of your tax settings right from your Square Dashboard or from the "settings" section of your Square Register App.
Within an Invoice you can control the tax on an item level. When creating an invoice, you should see an arrow next to your item. By clicking that little arrow, your tax options will drop down and you will be able to turn your tax on or off for each item in your invoice. I attached a screenshot that may help display this better. 
